Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,369,001 |
C→T |
52.5% |
V138V (GTG→GTA) |
dusC ← |
tRNA‑dihydrouridine synthase C |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,369,001 | 0 | C | T | 52.5%
| ‑2.1
/ 32.6
| 40 | V138V (GTG→GTA) | dusC | tRNA‑dihydrouridine synthase C |
| Reads supporting (aligned to +/- strand): ref base C (14/5); new base T (7/14); total (21/19) |
| Fisher's exact test for biased strand distribution p-value = 1.40e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.50e-01 |
CTGTTGAACCGCATCGGCGATTTCAAATTTCTTCTCACCGCTGTCCCAGCCCAGACGCACTTTCACGCTGACGGGCAAATGCGCCGGTACAGCTTCACGCATCGCTTTTGCACCCTGGTA > minE/1368938‑1369057
|
cTGTTGAACCGCATCGGCGATTTCAAATTTCTTCTCACCGCTGTCCCAGCCCAGACGCACTTTCACGCt < 1:2192671/69‑1 (MQ=255)
ggCGATTTCAAATTTCTTCTCACCGCTGTCCCAGCCCAGACGCACTTTCACGCTGACGGGCAAATgcgc > 1:1126132/1‑69 (MQ=255)
ggCGATTTCAAATTTCTTCTCACCGCTGTCCCAGCCCAGACGCACTTTCACGCTGACGGGCAAATgcgc > 1:33743/1‑69 (MQ=255)
ggCGATTTCAAATTTCTTCTCACCGCTGTCCCAGCCCAGACGCACTTTCACGCTGACGGGCAAATgcgc > 1:3323892/1‑69 (MQ=255)
ggCGATTTCAAATTTCTTCTCACCGCTGTCCCAGCCCAGACGCACTTTCACGCTGACGGGCAAATgcgc > 1:2989804/1‑69 (MQ=255)
ggCGATTTCAAATTTCTTCTCACCGCTGTCCCAGCCCAGACGCACTTTCACGCTGACGGGCAAATgcgc > 1:2680265/1‑69 (MQ=255)
ggCGATTTCAAATTTCTTCTCACCGCTGTCCCAGCCCAGACGCACTTTCACGCTGACGGGCAAATgcgc > 1:2671501/1‑69 (MQ=255)
ggCGATTTCAAATTTCTTCTCACCGCTGTCCCAGCCCAGACGCACTTTCACGCTGACGGGCAAATgcgc > 1:2399060/1‑69 (MQ=255)
ggCGATTTCAAATTTCTTCTCACCGCTGTCCCAGCCCAGACGCACTTTCACGCTGACGGGCAAATgcgc > 1:2365599/1‑69 (MQ=255)
ggCGATTTCAAATTTCTTCTCACCGCTGTCCCAGCCCAGACGCACTTTCACGCTGACGGGCAAATgcgc > 1:2113442/1‑69 (MQ=255)
ggCGATTTCAAATTTCTTCTCACCGCTGTCCCAGCCCAGACGCACTTTCACGCTGACGGGCAAATgcgc > 1:1690178/1‑69 (MQ=255)
ggCGATTTCAAATTTCTTCTCACCGCTGTCCCAGCCCAGACGCACTTTCACGCTGACGGGCAAATgcgc > 1:157936/1‑69 (MQ=255)
ggCGATTTCAAATTTCTTCTCACCGCTGTCCCAGCCCAGACGCACTTTCACGCTGACGGGCAAATgcgc > 1:1477482/1‑69 (MQ=255)
ggCGATTTCAAATTTCTTCTCACAGCTGTCCCAGCCCAGACGCACTTTCACGCTGACGGGCAAATgcgc > 1:366410/1‑69 (MQ=255)
ggCGATTTCAAAATTCTTCTCACCGCTGTCCCAGCCCAGACGCACTTTCACGCTGACGGGCAAATgcg > 1:1858093/1‑68 (MQ=255)
ttCAAATTTCTTCTCACCGCTGTCCCAGCCCAGACGCACTTTCACGCTGACGGGCAAATGCGCCGGTAc < 1:46711/69‑1 (MQ=255)
agcccagACGCACTTTTACGCTGACAGGCAAATGCGCCGGTACAGCTTCGCGCATCGCTTTTGCACCCt > 1:892749/1‑69 (MQ=255)
agcccagACGCACTTTTACGCTGACAGGCAAATGCGCCGGTACAGCTTCGCGCATCGCTTTTGCACCCt > 1:86066/1‑69 (MQ=255)
agcccagACGCACTTTTACGCTGACAGGCAAATGCGCCGGTACAGCTTCGCGCATCGCTTTTGCACCCt > 1:105164/1‑69 (MQ=255)
agcccagACGCACTTTTACGCTGACAGGCAAATGCGCCGGTACAGCTTCGCGCATCGCTTTTGCACCCt > 1:1130756/1‑69 (MQ=255)
agcccagACGCACTTTTACGCTGACAGGCAAATGCGCCGGTACAGCTTCGCGCATCGCTTTTGCACCCt > 1:123344/1‑69 (MQ=255)
agcccagACGCACTTTTACGCTGACAGGCAAATGCGCCGGTACAGCTTCGCGCATCGCTTTTGCACCCt > 1:1514656/1‑69 (MQ=255)
agcccagACGCACTTTTACGCTGACAGGCAAATGCGCCGGTACAGCTTCGCGCATCGCTTTTGCACCCt > 1:1289747/1‑69 (MQ=255)
cagACGCACTTTTACGCTGACAGGCAAATGCGCCGGTACAGCTTCGCGCATCGCTTTTGCACCCTGGTa < 1:2582926/69‑1 (MQ=255)
cagACGCACTTTTACGCTGACAGGCAAATGCGCCGGTACAGCTTCGCGCATCGCTTTTGCACCCTGGTa < 1:2239519/69‑1 (MQ=255)
cagACGCACTTTTACGCTGACAGGCAAATGCGCCGGTACAGCTTCGCGCATCGCTTTTGCACCCTGGTa < 1:876853/69‑1 (MQ=255)
cagACGCACTTTTACGCTGACAGGCAAATGCGCCGGTACAGCTTCGCGCATCGCTTTTGCACCCTGGTa < 1:678009/69‑1 (MQ=255)
cagACGCACTTTTACGCTGACAGGCAAATGCGCCGGTACAGCTTCGCGCATCGCTTTTGCACCCTGGTa < 1:592353/69‑1 (MQ=255)
cagACGCACTTTTACGCTGACAGGCAAATGCGCCGGTACAGCTTCGCGCATCGCTTTTGCACCCTGGTa < 1:2543595/69‑1 (MQ=255)
cagACGCACTTTTACGCTGACAGGCAAATGCGCCGGTACAGCTTCGCGCATCGCTTTTGCACCCTGGTa < 1:1283950/69‑1 (MQ=255)
cagACGCACTTTTACGCTGACAGGCAAATGCGCCGGTACAGCTTCGCGCATCGCTTTTGCACCCTGGTa < 1:2584032/69‑1 (MQ=255)
cagACGCACTTTTACGCTGACAGGCAAATGCGCCGGTACAGCTTCGCGCATCGCTTTTGCACCCTGGTa < 1:320277/69‑1 (MQ=255)
cagACGCACTTTTACGCTGACAGGCAAATGCGCCGGTACAGCTTCGCGCATCGCTTTTGCACCCTGGTa < 1:3185724/69‑1 (MQ=255)
cagACGCACTTTTACGCTGACAGGCAAATGCGCCGGTACAGCTTCGCGCATCGCTTTTGCACCCTGGTa < 1:3092281/69‑1 (MQ=255)
cagACGCACTTTTACGCTGACAGGCAAATGCGCCGGTACAGCTTCGCGCATCGCTTTTGCACCCTGGTa < 1:2919236/69‑1 (MQ=255)
cagACGCACTTTTACGCTGACAGGCAAATGCGCCAGTACAGCTTCGCGCATCGCTTTTGCACCCTGGTa < 1:2982485/69‑1 (MQ=255)
cagACGCACTTTCACGCTGACGGGCAAATGCGCCGGTACAGCTTCACGCATCGCTTTTGCACCCTGGTa < 1:257481/69‑1 (MQ=255)
agACGCACTTTTACTCTGACAGGCAAATGCGCCGGTACAGCTTCGCGCATCGCTTTTGCACCCTGGTa < 1:2792646/68‑1 (MQ=255)
agACGCACTTTCACGCTGACGGGCAAATGCGCCGGTACAGCTTCACGCATCGCTTTTGCACCCTGGTa < 1:477441/68‑1 (MQ=255)
agACGCACTTTCACGCTGACGGGCAAATGCGCCGGTACAGCTTCACGCATCGCTTTTGCACCCTGGTa < 1:502713/68‑1 (MQ=255)
|
CTGTTGAACCGCATCGGCGATTTCAAATTTCTTCTCACCGCTGTCCCAGCCCAGACGCACTTTCACGCTGACGGGCAAATGCGCCGGTACAGCTTCACGCATCGCTTTTGCACCCTGGTA > minE/1368938‑1369057
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
